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- PDB-4l0y: Crystal structure of Runx1 and Ets1 bound to TCR alpha promoter (... -

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Basic information

Entry
Database: PDB / ID: 4l0y
TitleCrystal structure of Runx1 and Ets1 bound to TCR alpha promoter (crystal form 1)
Components
  • 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'
  • 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'
  • Protein C-ets-1
  • Runt-related transcription factor 1
KeywordsTRANSCRIPTION/DNA / RUNT domain / ETS domain / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of hair follicle cell proliferation / Organic cation transport / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation ...regulation of hair follicle cell proliferation / Organic cation transport / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / core-binding factor complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of CD8-positive, alpha-beta T cell differentiation / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / PML body organization / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / definitive hemopoiesis / regulation of T cell anergy / positive regulation of leukocyte adhesion to vascular endothelial cell / embryonic hemopoiesis / hair follicle morphogenesis / regulation of cell differentiation / behavioral response to pain / hemopoiesis / negative regulation of cell cycle / basement membrane / regulation of signal transduction / neuron development / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / regulation of angiogenesis / response to retinoic acid / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / ossification / liver development / transcription corepressor binding / nuclear receptor coactivator activity / skeletal system development / central nervous system development / cell motility / promoter-specific chromatin binding / neuron differentiation / Oncogene Induced Senescence / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of type II interferon production / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Protein C-ets-1, pointed domain / Transforming protein C-ets ...Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1 / Runt-related transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTahirov, T.H.
CitationJournal: Leukemia / Year: 2014
Title: Structural basis of Ets1 activation by Runx1.
Authors: Shrivastava, T. / Mino, K. / Babayeva, N.D. / Baranovskaya, O.I. / Rizzino, A. / Tahirov, T.H.
History
DepositionJun 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Runt-related transcription factor 1
B: Protein C-ets-1
C: 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'
D: 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'


Theoretical massNumber of molelcules
Total (without water)53,2634
Polymers53,2634
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-30 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.622, 138.945, 98.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Runt-related transcription factor 1 / Runx1 / Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / ...Runx1 / Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / Oncogene AML-1 / Polyomavirus enhancer-binding protein 2 alpha B subunit / PEA2-alpha B / PEBP2-alpha B / SL3-3 enhancer factor 1 alpha B subunit / SL3/AKV core-binding factor alpha B subunit


Mass: 26492.076 Da / Num. of mol.: 1 / Fragment: UNP residues 1-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Runx1, Aml1, Cbfa2, Pebp2ab / Production host: Escherichia coli (E. coli) / References: UniProt: Q03347
#2: Protein Protein C-ets-1 / Ets1 / p54


Mass: 16973.369 Da / Num. of mol.: 1 / Fragment: UNP residues 296-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS1, EWSR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14921
#3: DNA chain 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'


Mass: 4843.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TCR alpha DNA strand 1 / Source: (synth.) Homo sapiens (human)
#4: DNA chain 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'


Mass: 4954.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TCR alpha DNA strand 2 / Source: (synth.) Homo sapiens (human)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: Plate-shaped crystals grown from 100 mM potassium chloride, 15 mM magnesium chloride hexahydrate, 25 mM MES, pH 5.6, 14% v/v PEG550 MME, 6% v/v glycerol, crystal size improved by ...Details: Plate-shaped crystals grown from 100 mM potassium chloride, 15 mM magnesium chloride hexahydrate, 25 mM MES, pH 5.6, 14% v/v PEG550 MME, 6% v/v glycerol, crystal size improved by macroseeding, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 24213 / % possible obs: 98 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 2.9 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.7
Reflection shellResolution: 2.5→2.54 Å / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.67 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3478297.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1132 4.8 %RANDOM
Rwork0.225 ---
obs0.225 23493 95.1 %-
all-24213 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.1567 Å2 / ksol: 0.353554 e/Å3
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.51 Å20 Å2
3---0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 650 0 66 2584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 158 4.4 %
Rwork0.342 3458 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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